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SelectVariants hangs while filtering out the biallelic SNP's
The version of my JAVA is: 1.7.0_79
The version of my GATK is: 3.7.0
My OS is: Ubuntu 14.04.2 LTS
My processor is: Intel Core i5-4440 CPU @ 3.10GHz × 4
I have been successful in creating a vcf file using Unified Genotyper. This Vcf file was obtained from a merged bam.
Information about the bam files
The merged bam was obtained from 10 different bam files.(10 different samples but of same organism)
These individual bam files are not very big either ranging around 50-100 Mb and the merged bam is 368M in size.
The needful such as co-ordinate sorting and adding the readgroups have been done.
There has been no issues with them when checked with ValidateSamFile.
Information about the vcf file
The number of records in the vcf are 282931.
The command used for vcf file generation is:
java -jar /dummy/GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar -T UnifiedGenotyper -I Realign.bam -R REF.fasta -o Calling.vcf -glm BOTH
When I try to run SelectVaraints on the above vcf file, the time remaining for the process to complete as indicated in the log file is 1176.1 w.
The command used for filtering the biallelic SNP's is:
nohup java -jar /dummy/GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar -T SelectVariants --variant Calling.vcf -R REF.fasta -o Biallelic.vcf -restrictAllelesTo BIALLELIC &
What is going wrong here is evading me at this point.
The VCF file generation took around 2 days using UnifiedGenotyper but the filtering is just hanging.
How can I fasten this step and what may be sources of error for such a behaviour